5t05

Crystal structure of heparan sulfate 6-O-sulfotransferase with bound PAP and IdoA2S containing hexasaccharide substrate

Method: X-RAY DIFFRACTION Dmax: 136.7 Å Quality: GOOD

1. 蛋白身份与相关结构 Protein Identity & Related Structures

maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein

Danio rerio

UniProt A0MGZ7

当前结构中的状态

Assembly 聚集状态 构建体 突变与修饰 配体、离子与共同组分 实验方法与环境 结构质量
1 信息不足 单体 蛋白 × 1 其他聚合物 2 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 A; UniProt 75–395 突变:D82A, K83A, E172A, N173A, K239A, E359A, K362A, D363A ;2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid ; × 1 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 A3P ADENOSINE-3'-5'-DIPHOSPHATE × 1 NPO P-NITROPHENOL × 1 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 3 NA SODIUM ION × 5 TLA L(+)-TARTARIC ACID × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;100mM Tris pH 7.5, 200mM disodium tartrate, 18-19% PEG 3350, 1mM PAP, 5mM maltose, 10mM oligosaccharide ligand 分辨率 1.95 Å R-free 0.212
2 信息不足 单体 蛋白 × 1 其他聚合物 2 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 B; UniProt 75–395 突变:D82A, K83A, E172A, N173A, K239A, E359A, K362A, D363A ;2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid ; × 1 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 A3P ADENOSINE-3'-5'-DIPHOSPHATE × 1 NPO P-NITROPHENOL × 1 EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 1 NA SODIUM ION × 2 TLA L(+)-TARTARIC ACID × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;100mM Tris pH 7.5, 200mM disodium tartrate, 18-19% PEG 3350, 1mM PAP, 5mM maltose, 10mM oligosaccharide ligand 分辨率 1.95 Å R-free 0.212

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly, “相对当前条目”直接指出证据层面的不同;没有差异标签表示当前已读取字段一致。

共 2 个其他 PDB 条目、4 个 assembly。 打开独立比较页并筛选聚集状态

查看构建体与数据证据
UniProt名称 H6ST3_DANRE
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 372–692; UniProt 75–395 作者链 B; PDB构建体 372–692; UniProt 75–395

maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein

Danio rerio

UniProt P0AEY0

当前结构中的状态

Assembly 聚集状态 构建体 突变与修饰 配体、离子与共同组分 实验方法与环境 结构质量
1 信息不足 单体 蛋白 × 1 其他聚合物 2 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 A; UniProt 27–392 突变:D82A, K83A, E172A, N173A, K239A, E359A, K362A, D363A ;2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid ; × 1 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 A3P ADENOSINE-3'-5'-DIPHOSPHATE × 1 NPO P-NITROPHENOL × 1 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 3 NA SODIUM ION × 5 TLA L(+)-TARTARIC ACID × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;100mM Tris pH 7.5, 200mM disodium tartrate, 18-19% PEG 3350, 1mM PAP, 5mM maltose, 10mM oligosaccharide ligand 分辨率 1.95 Å R-free 0.212
2 信息不足 单体 蛋白 × 1 其他聚合物 2 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 B; UniProt 27–392 突变:D82A, K83A, E172A, N173A, K239A, E359A, K362A, D363A ;2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid ; × 1 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 A3P ADENOSINE-3'-5'-DIPHOSPHATE × 1 NPO P-NITROPHENOL × 1 EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 1 NA SODIUM ION × 2 TLA L(+)-TARTARIC ACID × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;100mM Tris pH 7.5, 200mM disodium tartrate, 18-19% PEG 3350, 1mM PAP, 5mM maltose, 10mM oligosaccharide ligand 分辨率 1.95 Å R-free 0.212

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly, “相对当前条目”直接指出证据层面的不同;没有差异标签表示当前已读取字段一致。

共 109 个其他 PDB 条目、147 个 assembly。 打开独立比较页并筛选聚集状态

查看构建体与数据证据
UniProt名称 MALE_ECO57
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 2–367; UniProt 27–392 作者链 B; PDB构建体 2–367; UniProt 27–392

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。 链映射与序列区间收在“数据证据”中;数据库内部编号、导入时间和 assembly 操作表达式仅用于维护,因此不在读者页面展示。

SAXS 散射曲线 SAXS Profile

SAXS profile for 5t05

P(r) 距离分布 P(r) Distribution

P(r) distribution for 5t05
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id5t05
沉积日期 deposition_date2016-08-15
结构标题 titleCrystal structure of heparan sulfate 6-O-sulfotransferase with bound PAP and IdoA2S containing hexasaccharide substrate
关键词 keywordsheparan sulfate, sulfotransferase, complex, TRANSFERASE; TRANSFERASE
实验方法 methodX-RAY DIFFRACTION

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier41.14
回转半径 Rg (电子) rg_electron40.19
零角强度 I(0) i0373912000.00
分子量 molecular_weight155630.0 kDa
排除体积 excluded_volume193610 ų
包络体积 envelope_volume259140 ų
水化壳体积 shell_volume54963 ų
包络直径 envelope_diameter152.6
壳层 Rg shell_rg44.37
包络 Rg envelope_rg39.75
形状 Rg shape_rg40.09
总 Rg total_rg40.77
总原子数 total_atoms10931
残基数 n_residues1347
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax136.7
Rg (实空间) rg_real41.20
Rg 误差 (实空间) rg_real_error1.61
I(0) (实空间) i0_real3.7390e+08
I(0) 误差 (实空间) i0_real_error7.0090e+06
Rg (倒空间) rg_reciprocal41.15
I(0) (倒空间) i0_reciprocal373900000.0000
解质量估计 total_estimate0.8152
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary50.3
偏度 Skewness skewness0.349
峰度 Kurtosis kurtosis-0.397
角度范围 angular_range— – 0.1900 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha73120000.0000
实空间数据点数 n_real_points39
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.872; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

5. 晶体学与实验 5. Crystallography & Experiment

6. 实体与聚合物信息 Entities & Polymers (10)

7. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

结构域编号 domain_id5t05A01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id5t05B01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases

8. 引用文献 (1)

9. 文件与曲线 (10)